8AVS

Racemic protein crystal structure of aureocin A53 from Staphylococcus aureus in the presence of citrate and acetate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	292	A racemic mixture of L-Aureocin A53 and D-Aureocin A53 at 40 mg/mL concentration was mixed 1:1 with 0.2 M ammonium acetate, 0.2 M sodium citrate and 29% PEG 4000 v/v precipitant condition, pH 5.6 in a 1 microlitre sitting drop. Crystals were submerged in 20% PEG 400 in the precipitant solution as cryoprotectant and flash frozen in liquid nitrogen during harvesting.

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.07	α = 90
b = 37.28	β = 93.05
c = 113.95	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2019-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9119	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.21	36.48	96.6	0.998	8.8	3.1		90457

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.21	1.23	80.3		0.617	1	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2N8O	1.21	36.48	90456	4505	96.37	0.189	0.187	0.2208	20.282

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-1.514		0.138	0.371		1.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.688
r_dihedral_angle_3_deg	10.956
r_dihedral_angle_1_deg	5.012
r_lrange_it	3.258
r_lrange_other	2.916
r_scangle_it	2.427
r_scangle_other	2.426
r_scbond_it	2.068
r_scbond_other	2.067
r_mcangle_other	1.903
r_mcangle_it	1.901
r_mcbond_it	1.596
r_mcbond_other	1.594
r_rigid_bond_restr	1.41
r_angle_refined_deg	1.339
r_angle_other_deg	1.263
r_nbd_other	0.302
r_nbd_refined	0.222
r_nbtor_refined	0.204
r_symmetry_nbd_refined	0.2
r_symmetry_nbd_other	0.166
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.093
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.026
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1704
Nucleic Acid Atoms
Solvent Atoms	387
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building